Advancing molecular bioscience

Then and now: Continuing our look at biochemistry in the 80s

In the 1980s a three-part series of videos was published by Portland Press on behalf of the Biochemical Society. ‘The Biochemical Basis of Biology’ video series aimed to present biochemical facts and concepts in a dynamic way to students in further and higher education.

To see how biochemistry knowledge and techniques have changed in the last 30 years, we asked members of the Biochemical Society to review these videos and to write a short text comparing them to where we are today.

Following on from Dr Helen Watson’s review of Cell Structure and Energy Production, today Dr Joanna Wilson (University of Glasgow) looks at the second video Manipulating DNA. Keep an eye out on our blog for a commentary on the final video, DNA and Protein Synthesis, in the coming weeks.

Manipulating DNA

Guest post by Dr Joanna Wilson, University of Glasgow

This video, made in 1994, shows some fundamental techniques in molecular biology, used to manipulate DNA. It is divided into four sections covering [1] restriction digestion (cutting DNA), [2] agarose gel electrophoresis (separating DNA fragments by size), [3] the polymerase chain reaction (PCR, used to amplify tiny quantities of DNA) and [4] cloning DNA (permitting archiving, production and manipulation of specific DNA fragments, as well as expression of genes). Although the video is now over 20 years old, the basic concepts described and many of the techniques used, are central to molecular biology and are still used in labs around the world today.

Some protocol aspects have changed since the making of this video, in particular the methods are now faster and safer, but approaches such as these have led to a revolution in molecular biology, such that, although still used, these techniques now form just one small part of a huge armoury of DNA technology.

So how exactly have the specific techniques shown improved today? Much of the equipment used, such as the powerpacks (for gel ecletrophoresis), the thermocycler (for PCR), the gel camera system, are more efficient, smaller, sleeker, usually computerised and certainly more versatile. For example, gel imaging systems are linked to computers now, for digital image production (instead of taking an analogue photo and having to produce an instamatic print). Thermocyclers have heated lids (no need for oil on top of the PCR sample) to prevent evaporation and maintain precise temperatures and they can be programmed to run multiple temperature parameters at once. Safety in molecular protocols has improved immensely over the past decades. For example, Bunson burners are almost a thing of the past; the method to spread bacteria on an agar plate using an ethanol and flame sterilised spreader – simply replaced now with a disposable plastic spreader (no open flame and alcohol). Although still widely used, several labs have replaced ethidium bromide (a nasty mutagen) to visualise DNA, with safer dyes. One of the biggest changes since 1994 is evident in the method to purify plasmid DNA. In section [4], we see how to make a caesium chloride density gradient to purify the plasmid. I winced when we were shown the use of a sharp needle to collect the DNA, full of mutagenic ethidium bromide, even though this was a method I used to conduct routinely. Just one needle slip would have been very nasty. So what do we use now? We buy a DNA purification kit from a biotechnology company, containing a little column to allow purification of the DNA by its charge (remember it is negative) and in a matter of an hour, we have nice clean DNA, no big ultra-centrifuge for over-night spins, no toxic and mutagenic substances – easy.

What about the molecular revolution? The protocol shown in the first section shows how to cut DNA in a test tube. The use of restriction enzymes is still a corner stone in the lab. But more than this, DNA can now be manipulated in almost every way imaginable. It can be cut, bits deleted or changed, glued, twisted and flipped, in a test tube and amazingly, even within a living cell. While the principles of PCR, shown in section [3], haven’t changed a jot, the enormity of PCR application was not realised at that time. For example, modern day forensics would be unrecognisable 20 years ago, when PCR was still in its infancy. Now an individual can be identified from a hair or speck of blood using PCR followed by “DNA fingerprinting”. Using PCR, even ancient DNA from Neanderthal man has been analysed and this allows us to work out the evolutionary relationship of Neanderthals with us. PCR and other DNA polymerisation wizardry has also revolutionised DNA sequencing. It took over 10 years to sequence the first human genome, now it takes just a few days and given enough sequencing machines, multiple genomes can be read at once. This exemplifies an area of major advancement in molecular biology. Many of the techniques that can be conducted by one person in a lab, as shown in the video, have advanced to the point where much can be automated and robotic machines conduct the work with very high throughput. The single scientist in the lab is far from redundant, but we can leave a lot of the boring work to machines and biotechnology companies and use kits to speed through our bright ideas.